Atomistry » Calcium » PDB 4gzt-4h82 » 4h0n
Atomistry »
  Calcium »
    PDB 4gzt-4h82 »
      4h0n »

Calcium in PDB 4h0n: Crystal Structure of Spodoptera Frugiperda DNMT2 E260A/E261A/K263A Mutant

Protein crystallography data

The structure of Crystal Structure of Spodoptera Frugiperda DNMT2 E260A/E261A/K263A Mutant, PDB code: 4h0n was solved by S.Li, J.Du, H.Yang, J.Yin, J.Zhong, J.Ding, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.70 / 2.71
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 97.394, 106.154, 151.016, 90.00, 90.00, 90.00
R / Rfree (%) 20.2 / 25.6

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Spodoptera Frugiperda DNMT2 E260A/E261A/K263A Mutant (pdb code 4h0n). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Spodoptera Frugiperda DNMT2 E260A/E261A/K263A Mutant, PDB code: 4h0n:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 4h0n

Go back to Calcium Binding Sites List in 4h0n
Calcium binding site 1 out of 4 in the Crystal Structure of Spodoptera Frugiperda DNMT2 E260A/E261A/K263A Mutant


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Spodoptera Frugiperda DNMT2 E260A/E261A/K263A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:47.4
occ:1.00
OD1 A:ASP106 2.5 52.7 1.0
O A:GLY103 2.9 38.1 1.0
OD2 A:ASP106 3.0 34.2 1.0
CG A:ASP106 3.1 44.9 1.0
C A:GLY103 3.8 33.0 1.0
NZ A:LYS134 4.1 22.6 1.0
OE1 A:GLN107 4.2 0.7 1.0
CD A:GLN107 4.3 94.5 1.0
CB A:ASP106 4.5 52.1 1.0
CA A:GLY103 4.6 30.8 1.0
NE2 A:GLN107 4.6 89.2 1.0
N A:ILE104 4.6 23.1 1.0
CA A:ILE104 4.6 23.9 1.0
CG A:GLN107 4.9 82.4 1.0

Calcium binding site 2 out of 4 in 4h0n

Go back to Calcium Binding Sites List in 4h0n
Calcium binding site 2 out of 4 in the Crystal Structure of Spodoptera Frugiperda DNMT2 E260A/E261A/K263A Mutant


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Spodoptera Frugiperda DNMT2 E260A/E261A/K263A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca402

b:64.3
occ:1.00
O B:GLY103 2.9 28.3 1.0
NE2 B:GLN107 3.1 78.5 1.0
OD1 B:ASP106 3.5 70.4 1.0
C B:GLY103 3.7 27.3 1.0
CG B:GLN107 3.7 62.2 1.0
CD B:GLN107 3.8 77.1 1.0
OD2 B:ASP106 3.8 72.1 1.0
CA B:ILE104 3.8 29.8 1.0
CG B:ASP106 4.0 66.9 1.0
N B:ILE104 4.1 25.7 1.0
CG2 B:ILE104 4.6 39.5 1.0
C B:ILE104 4.7 34.6 1.0
CB B:ILE104 4.7 37.0 1.0
CA B:GLY103 4.7 34.8 1.0
OE1 B:GLN107 4.9 84.0 1.0

Calcium binding site 3 out of 4 in 4h0n

Go back to Calcium Binding Sites List in 4h0n
Calcium binding site 3 out of 4 in the Crystal Structure of Spodoptera Frugiperda DNMT2 E260A/E261A/K263A Mutant


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Spodoptera Frugiperda DNMT2 E260A/E261A/K263A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca402

b:62.9
occ:1.00
O C:GLY103 3.0 51.5 1.0
OD1 C:ASP106 3.0 53.9 1.0
C C:GLY103 3.8 46.4 1.0
CG C:ASP106 3.8 48.6 1.0
OD2 C:ASP106 3.8 39.4 1.0
CA C:ILE104 4.1 30.1 1.0
N C:ILE104 4.3 27.5 1.0
CG C:GLN107 4.6 66.0 1.0
CA C:GLY103 4.7 40.6 1.0
C C:ILE104 4.9 30.5 1.0

Calcium binding site 4 out of 4 in 4h0n

Go back to Calcium Binding Sites List in 4h0n
Calcium binding site 4 out of 4 in the Crystal Structure of Spodoptera Frugiperda DNMT2 E260A/E261A/K263A Mutant


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Spodoptera Frugiperda DNMT2 E260A/E261A/K263A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca402

b:62.2
occ:1.00
OD1 D:ASP106 2.3 94.5 1.0
O D:GLY103 2.5 52.0 1.0
CG D:ASP106 3.4 96.5 1.0
C D:GLY103 3.4 48.8 1.0
CB D:ASP106 3.9 82.0 1.0
CA D:ILE104 4.2 40.1 1.0
N D:ILE104 4.2 44.3 1.0
CA D:GLY103 4.3 49.2 1.0
OD2 D:ASP106 4.4 0.8 1.0
C D:ILE104 4.8 37.9 1.0
N D:ASP106 4.8 58.9 1.0

Reference:

S.Li, J.Du, H.Yang, J.Yin, J.Ding, J.Zhong. Functional and Structural Characterization of DNMT2 From Spodoptera Frugiperda. J Mol Cell Biol V. 5 64 2013.
ISSN: ISSN 1674-2788
PubMed: 23103599
DOI: 10.1093/JMCB/MJS057
Page generated: Sat Dec 12 04:49:29 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy